The pseudo-science site Answers In Genesis has listed 12 argument against evolution. Here are my comments on each of them.
1. Evolution is a fact
"Unobservable past" - It depends on what do we mean by observation. If it only means watching events unfold first hand, of course we cannot be in the past to observe. However, events in the past usually left evidences behind. It is like solving a murder case, evidence can reconstruct the past.
Evolution is a scientific theory meaning it "explains" facts, it predicts observation which can be factually verified. It is built upon tons of observations. Many creationists agree that evolution occurs, as demonstrated in selection by human such as breeding of dogs or plants. Darwin's evolution is just an extension to the "micro evolutions" coined by the creationists. What nature has is time. Given sufficient time, the survival niche exploited by different organisms created the complexity and diversity we can observe today. Evolution by natural selection is now the foundation of modern biology.
2. Only the uneducated reject evolution
AIG makes a fact sounds like an arrogant announcement. Yes, only the uneducated today reject evolution. Quoting Newton does not advance the AIG argument a single bit. Newton did not know about Evolution by natural selection. Darwin's theory was published after Newton's death. Anyone, today, with a proper education in science should understand the role evolution has played.
3 Overwhelming evidence in all fields of science supports evolution
The AIG argument is that all the evidence before Darwin was there and unchanged. Only the views have changed. Yes, this is correct. Before Darwin, the available evidence superimposed by a biblical bias produces a different view from Darwin. That's why Darwin theory of evolution was controversial then and now. However, in the last 150 years since the publication of the theory, large amount of evidences have been added to the pool and the theory is growing ever stronger.
4 Doubting evolution is like doubting gravity
The straw man argument is 'Next, make a single-celled organism—like an amoeba—turn into a goat. Go ahead. We’ll wait.'. Well, there are dog domestication, rice and lots of examples. While science cannot modify an amoeba to a goat, biological science based on evolution has created wonderful approaches to medicine and many other fields.
5 Doubting evolution is like believing the earth is flat
WOW, what can I say. Yes, doubting evolution is like believing the earth is flat. Period.
6 It’s here, so it must have evolved
The argument was "A conclusion does not prove the premises are true. That is, if the answer is “four,” we could arrive at that any number of ways: 2 + 2, 5 - 1, etc. In the same way, evolutionists often assume that since certain species or traits exist, this is proof of evolution because that’s how it must have happened."
Yes, a single data point does not give support to such a complex theory. But when all the evidence are considered together, there is one reasonable explanation. In contrast, the creation story in Genesis does not explain anything. According to the Genesis, there would be a global flood at Noah's time. How does it explain the different animals in today's Australia? How does it explain all the virus and bacteria? Where is the evidence of the Ark? Why geological data contradicts with that story? Why carbon dating invalidates the Genesis's time line? Oh, god like to joke with us or the all mighty cannot stop Satan from putting in false evidences.
7 Natural selection is evolution
The AIG confuses abiogenesis with evolution. The origin of life is a different research domain. How life started is still unknown. The honest answer is "we do not know". It is just plain stupid to replace an honest answer with the creation story, which has no evidential support and of which the origin is problematic.
8 Common design means common ancestry
"A common Designer fits the evidence just as well, if not better." Who designed the designer?
9 Sedimentary layers show millions of years of geological activity
"Sedimentary layers show one thing: sedimentary layers. In other words, we can—and should—study the rocks, but the claim that rocks prove the earth must be billions of years old ignores one important point: such an interpretation is built upon a stack of assumptions. When we start from the Bible and examine the rocks within the framework of a global Flood, the need for long ages vanishes."
Well, the need for long ages vanishes in the creation story of the Genesis. And that's exactly the problem. The dating of the rocks, biological remains and so on indicated it took a long time. Why the designer needs such a long time and yet give a short version of the creation story?
10 Mutations drive evolution
" Mutations cannot produce the types of changes evolution requires—not even close. Some may benefit an organism (e.g., beetles on a windy island losing wings), but virtually every time mutations come with a cost." Yes, many mutations resulted in losing the survival edge. But every now and then, some say help the survival just that little bit and such mutation gets reproduced. The accumulation of mutations drives the evolution. The natural selection process drives the evolution. They go hand in hand.
11 The Scopes trial
No comment on this one. This is a legal case in USA.
12 Science vs religion
Every time when there is an overlap between science and religion, science wins. So will Darwin's theory of evolution. Time will tell.
Another comment can be found here.